/*
 * This file is part of the Popitam software
 * Copyright (C) 2009 Swiss Institute of Bioinformatics
 *
 * This program is free software; you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation; either version 2 of the License, or
 * (at your option) any later version.
 *
 * This program is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with this program; if not, write to the Free Software
 * Foundation, Inc., 59 Temple Place, Suite 330, 
 * Boston, MA 02111-1307, USA.
 */

#ifndef __ANTS_H__
#define __ANTS_H__

// ****************************************************************************

#include "defines.h"
#include "runManagerParameters.h"
#include "aa.h"

// ****************************************************************************

class ants {
  public :

  runManagerParameters *runManParam;
  aa                   *aaParam;

  int               startVertex;
  int               iPlace;               
 
  int               iSuffPlace;           // indice dans l'arbre (le tab) des suffixes
  int               arcPos;               // position sur l'arc dans le suffTree (suffTab)

//  bool              tabooTab[MAX_PEAKS];
  PATH              runnedVertex[MAX_LENGHT];
  char              parsedSequence[MAX_LENGHT];
  int               runnedVertexNb;
  int               parsedSequenceLenght;

  public :
  ants();
  ~ants();  
  void  init(runManagerParameters*, aa*, char*, float);
};


// ****************************************************************************

#endif
